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Downloads and Upgrades: Strand NGS, Reactome Pathway Browser, and More


Strand Life Sciences has released version 2.0 of its next-generation sequencing data analysis and visualization platform, Avadis NGS, which it has renamed Strand NGS.

The release combines features from Avadis NGS and the GeneSpring NGS. It includes a methyl-seq workflow, direct access to BioCyc and WikiPathways, better support for target enrichment experiments, and multi-omic pathway analysis.

The developers of the Reactome database have a new Reactome Pathway Browser that provides an integrated suite of tools for pathway analysis.

Features in the tool let users map protein lists to Reactome pathways, perform pathway over representation analysis for gene sets, colorize pathway diagrams with gene expression data, and compare model organism and human pathways.

BioJava Legacy 1.9.0 is now available from the project page and from the maven central repository.

A new version of RINalyzer for Cytoscape 3.1 is available. RINalyzer is a tool for analyzing and visualizing residue interaction networks (RIN) that are generatedfrom 3D protein structures. This new version of the tool includes automatic import, generation, and annotation of RINs as well as new and user-friendly means to explore and compare RINs.

Also, the Resource for Biocomputing, Visualization, and Informatics group at the University of California, San Francisco have released cddApp, a Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites from the National Center for Biotechnology Information's Conserved Domain Database